Contacts of the strand formed by residues 150 - 153 (chain C) in PDB entry 2X1W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C VAL* 3.5 46.4 - - + +
147C ALA* 3.4 7.6 + - - +
149C ASN* 1.3 85.9 + - - +
151C PHE* 1.3 64.8 + - - +
152C PHE* 4.2 5.3 - - + -
187C GLU* 3.4 39.5 + - + +
188C ILE 3.4 5.2 - - - +
189C THR* 3.8 11.2 + - - +
1216C CS 3.6 13.2 - - - -
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Residues in contact with PHE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR 4.3 11.4 - - - -
149C ASN 3.4 15.9 - - - -
150C THR* 1.3 75.0 - - - +
152C PHE* 1.3 68.5 + - - +
153C LYS* 5.1 11.0 - - - -
187C GLU* 3.6 4.9 - - - +
188C ILE* 2.8 42.6 + - + +
190C VAL* 3.6 38.1 - - + -
1216C CS 4.1 11.9 - - - -
169D GLU* 2.8 41.1 - - + -
253O ASN* 5.5 9.4 - - - -
286O LYS* 4.4 10.1 - - - -
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Residues in contact with PHE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.3 46.4 - - + -
141C GLY* 3.8 23.3 - - - -
144C PHE* 6.5 1.1 - - + -
146C VAL* 3.9 27.8 - - + -
150C THR* 4.2 3.6 - - + -
151C PHE* 1.3 78.1 - - - +
153C LYS* 1.3 70.5 + - - +
154C PRO 3.2 5.6 - - - +
155C PRO* 3.1 23.5 - - + +
185C LEU* 4.4 12.8 - - + -
186C PHE 3.4 5.2 - - - +
187C GLU* 3.5 38.6 - - + -
199C VAL* 4.4 10.1 - - + -
201C ILE* 4.5 9.4 - - + -
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C PHE* 5.1 11.8 - - - -
152C PHE* 1.3 81.9 - - - +
154C PRO* 1.3 62.8 - - + +
155C PRO* 5.2 4.6 - - + +
186C PHE* 2.7 47.4 + - + +
188C ILE* 3.9 30.3 - - + -
126D TRP* 3.7 15.0 - - + +
167D ASN* 2.8 34.0 + - + +
168D SER* 5.0 1.0 - - - +
215O ILE* 4.5 14.1 - - + -
216O VAL 4.4 18.9 + - - +
217O VAL* 4.7 7.6 - - + -
218O VAL* 4.5 14.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il